[mira_talk] Re: Mira results much worse than newbler
- From: "Bastien Chevreux" <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 16 Jul 2011 09:26:15 +0200 (MEST)
> Betreff: [mira_talk] Re: Mira results much worse than newbler
> Maybe this is the only one but I had a bear of a time getting this
> one to work, and I expected that it wasn't a bug but just how sff_extract
> worked.
> The SRA sample SRR054580 demonstrates it though.
A specific SRA ... now we're getting somewhere.
> Since it was in the SRA I couldn't contact the sequence provider, evidently
> using minleft clip does exactly that. However going back and trying it on
> other sequences it does indeed seem to do exactly the same as sffinfo when it
> works.
It's not "when" sff_extract works ... when extracting non-paired sequences it
*always* works like sffinfo.
> ********************************************************************************
> WARNING: weird sequences in file SRR054580.sff
> After applying left clips, 513937 sequences (=57%) start with these bases:
> A
>
> This does not look sane.
> ...
This warning message is courtesy of sff_extract: the SFF is very probably
broken. sff_extract caught that and gave you a warning, which, by the way, you
do not get in sffinfo. The resulting FASTA file both from sffinfo and
sff_extract are still exactly the same.
B.
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